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. 2025 Jan 6;53(D1):D1243-D1249.
doi: 10.1093/nar/gkae974.

The UCSC Genome Browser database: 2025 update

Gerardo Perez  1 , Galt P Barber  1 , Anna Benet-Pages  2   3 , Jonathan Casper  1 , Hiram Clawson  1 , Mark Diekhans  1 , Clay Fischer  1 , Jairo Navarro Gonzalez  1 , Angie S Hinrichs  1 , Christopher M Lee  1 , Luis R Nassar  1 , Brian J Raney  1 , Matthew L Speir  1 , Marijke J van Baren  1 , Charles J Vaske  1 , David Haussler  1 , W James Kent  1 , Maximilian Haeussler  1
Affiliations

The UCSC Genome Browser database: 2025 update

Gerardo Perez et al. Nucleic Acids Res. .

Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) is a widely utilized web-based tool for visualization and analysis of genomic data, encompassing over 4000 assemblies from diverse organisms. Since its release in 2001, it has become an essential resource for genomics and bioinformatics research. Annotation data available on Genome Browser includes both internally created and maintained tracks as well as custom tracks and track hubs provided by the research community. This last year's updates include over 25 new annotation tracks such as the gnomAD 4.1 track on the human GRCh38/hg38 assembly, the addition of three new public hubs, and significant expansions to the Genome Archive[GenArk) system for interacting with the enormous variety of assemblies. We have also made improvements to our interface, including updates to the browser graphic page, such as a new popup dialog feature that now displays item details without requiring navigation away from the main Genome Browser page. GenePred tracks have been upgraded with right-click options for zooming and precise navigation, along with enhanced mouseOver functions. Additional improvements include a new grouping feature for track hubs and hub description info links. A new tutorial focusing on Clinical Genetics has also been added to the UCSC Genome Browser.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
(A) MANE transcripts displayed as the top result. (B) MANE transcript color for the tumor suppressor ‘BRCA1’ gene in the Genome Browser display.
Figure 2.
Figure 2.
(A) previous browser graphic page. (B) current browser graphic page displays trash icons next to custom tracks, more track columns on wider screens, increased font sizes for dialog boxes, and a reduction in text on the page.
Figure 3.
Figure 3.
The new popup dialog box that shows item details for the hg38 GENCODE ‘KnownGene’ track.
Figure 4.
Figure 4.
(A) Right-click options for genePred tracks. (B) Exon mouse over display for genePred tracks.
Figure 5.
Figure 5.
Search box shows the five most recent search terms.
Figure 6.
Figure 6.
Grouping of track hubs on the browser graphic page.
Figure 7.
Figure 7.
Extended DNA case/color options for a track hub.
See this image and copyright information in PMC

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